“Bioconductor Notes” published in The R Journal.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. The project has entered its twentieth year, with funding for core development and infrastructure maintenance secured through 2025 (NIH NHGRI 2U24HG004059). Additional support is provided by NIH NCI, Chan-Zuckerberg Initiative, National Science Foundation, Microsoft, and Amazon. In this news report, we give some updates on core team and project activities.
The current Bioconductor release is 3.16. It is compatible with R 4.2 and consists of 2183 software packages, 416 experiment data packages, 909 up-to-date annotation packages, 28 workflows, and 3 books. are built regularly from source and therefore fully reproducible; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.
We’re excited to introduce BiocPy, a project aimed at enabling Bioconductor workflows in Python. Analysts today use a variety of languages in their workflows, including R/Bioconductor for statistical analysis and Python for imaging or machine learning tasks. BiocPy aims to facilitate interoperability between R and Python by providing standardized data structures based on existing Bioconductor data structures. These include genomic ranges for interval based operations, summarized experiments and other derivatives for analyzing genomic experiments. To learn more, visit the BiocPy GitHub organization.
The default branch (that corresponds to Bioconductor devel version) will be renamed to devel on git.bioconductor.org for all packages to move forward with diversity and inclusiveness. The core has been doing extensive testing and is ready to move forward within the next 2-3 weeks.
Maintainers will temporarily still be able to push to either devel or master to allow time for adaptation, with the goal of eventually making it an error in maybe 2-3 release cycles (1-1.5 years) We will be making announcements on bioc-devel mailing list, Twitter, Mastodon, Slack, etc with an upcoming/heads up and an announcement when it is live.
Bioconductor participated as a mentoring community in Outreachy’s December 2022 - March 2023 internship round. Outreachy provides open source and open science internships to individuals impacted by systemic bias and underrepresentation in tech. Bioconductor received funding for two interns through Outreachy’s general fund for two projects. Kirabo Atuhurira, a software engineering student from Kampala, Uganda, was chosen to work on the BSgenomeForge, which attempts to simplify making Bsgenome data packages. Beryl Kanali, a masters student from Nairobi, Kenya, was chosen to work on Sweave2Rmd, which attempts to modernize Sweave vignettes by converting them into R Markdown. You can read more about their experience at Our experience as Outreachy interns with Bioconductor.
Bioconductor will also participate in Outreachy’s May 2023 - August 2023 internship round to offer internships with Bioconductor community projects.
The BioC2023 and EuroBioC2023 conferences have both been announced, and abstract submissions are open. BioC Asia 2023 will be announced later this year.
BioC2023 will be held in Boston, USA from Aug 2-4. Abstracts can be submitted until March 19.
EuroBioC2023 will be held in Ghent, Belgium from Sep 20-22. Abstracts can be submitted until April 14.
The Bioconductor blog is used for articles of interest by and for the community. Recent articles include:
Bioconductor Carpentries instructors Year 1
An update on the Bioconductor Carpentries global training program - applicants selected for Year 1
Introducing CuratedAtlasQueryR package
CuratedAtlasQueryR is a new package that enables easy programmatic exploration of CELLxGENE single-cell human cell atlas data.
Our experience as Outreachy interns with Bioconductor
Bioconductor participated in the Outreachy Internship program for the December 2022 cohort. Our interns share their experience working on their various projects and Bioconductor in general.
Bioconductor Hacktoberfest 2022 review and looking ahead to 2023
Last October, Bioconductor joined Hacktoberfest and got great community contributions there. Here, we describe its success and notify the community we plan to participate in 2023.
The Community Advisory Board (CAB) are voting in new members. Outgoing members are Susan Holmes, Leonardo Collado-Torres, Yagoub A. I. Adam, Matt Ritchie, Benilton Carvalho, we gratefully thank them for their service.
There is a Call for Bioconductor Community-Led events supported by the CAB. Apply in this form
If you are interested in becoming involved with one of these groups please contact the group leader(s).
Cloud Methods held their first meeting Feb 2023. The working group will meet monthly to develop standards and tools for the Bioconductor community related to the cloud.
Social media working group. A new group, started in Feb 2023, have set up Bioconductor Mastodon acccount.
Website working group are planning the redesign of bioconductor.org.
Start using Bioconductor by installing the most recent version of R and evaluating the commands
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install()Install additional packages and dependencies, e.g., SingleCellExperiment, with
BiocManager::install("SingleCellExperiment")Docker images provides a very effective on-ramp for power users to rapidly obtain access to standardized and scalable computing environments. Key resources include:
Upcoming and recently completed events are browsable at our events page.
The Technical and and Community Advisory Boards provide guidance to ensure that the project addresses leading-edge biological problems with advanced technical approaches, and adopts practices (such as a project-wide Code of Conduct that encourages all to participate. We look forward to welcoming you!
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".
For attribution, please cite this work as
Doyle & Team, "Bioconductor Notes", The R Journal, 2022
BibTeX citation
@article{RJ-2022-4-bioconductor,
author = {Doyle, Maria and Team, Bioconductor Core Developer},
title = {Bioconductor Notes},
journal = {The R Journal},
year = {2022},
note = {https://journal.r-project.org/news/RJ-2022-4-bioconductor},
volume = {14},
issue = {4},
issn = {2073-4859},
pages = {352-355}
}